The Clones were fielded after 9 years after their birth. They had accelerated learning and of course physically they were 18, but they were still essentially children when they started their journey as soldiers. Under the command of the Jedi they were instilled with a lot of the Jedi's values and even in the cases where the Jedi were bad commanders they were still influenced by the Jedi, heavily. Yes, Order 66 made them execute the Jedi, but I believe Palpatine would have seen them as still "tainted" by the Jedi. So, I think that's one reason.
The other reason was that the Clones had filled their purpose. If you read the Darth Plagueis novel it's very clear that the acquisition of the clones from Kamino had less to do with their quality as soldiers as more to do with the fact that they could be programed to kill the Jedi. Once Order 66 can been carried out they had filled their purpose. The Clone Wars was never really a true conflict since Palpatine controlled both sides and so it was shut down and the focus became control of the Galaxy, which Palpatine couldn't do with Clones since Kamino would never be able to produce them in the numbers required to garrison every world in the Empire.
I also think, that we're going to see a Clone Rebellion, that sadly, will be short lived. Many of the Clone fought very hard for their individuality, they believed strongly in the Republic, and there are definitely a few legions that were very loyal to the Jedi. All of these things were taken away from them by the Empire. I think we'll see via "Bad Batch" that about half of the clones, if not more, are going to end up in full on rebellion and likely most of them will be destroyed leaving very few clones left in the Imperial Stormtrooper core. With the accelerated aging many will be retired and we're already seeing in "Bad Batch" that a lot of clones are just deserting due to the low moral (Empire is treating them like shit) and some are coming to grips with what happened to them with Order 66.